Directory SL/PTCLEAN/

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westram 2022-08-03 15:52 Rev.: 19206

* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

6 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+6 -1)

westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1)

westram 2019-10-08 17:51 Rev.: 18159

* full update from child 'fix' into 'trunk'
- fix item name accessors ({{{GBT_get_name}}} + {{{GBT_get_name_or_description}}})
- add {{{null2empty}}}
* adds: log:branches/fix@18140:18158

2 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+2 -2)

westram 2019-07-17 16:22 Rev.: 17980

* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.

2 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+2 -3)

westram 2019-04-03 14:47 Rev.: 17738

* reintegrates 'config' into 'trunk'
* adds: log:branches/config@17733:17737

7 lines of code changed in 2 files:

• SL/PTCLEAN: ptclean.cxx (+6 -8), ptclean.h (+1 -6)

westram 2017-11-28 18:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

3 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+3 -3)

westram 2017-11-17 13:54 Rev.: 16668

* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

1 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+1)

westram 2016-08-11 11:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1)

westram 2015-01-23 15:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2014-11-17 16:42 Rev.: 13191

* reintegrates 'slv' into 'trunk'
* performs #624
* adds:
- log:branches/slv@13152:13190

4 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+4 -3)

westram 2014-08-27 12:21 Rev.: 12783

* publish TESTs for which nm 2.24 fails to export source location

1 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+1)

westram 2013-11-03 15:42 Rev.: 11060

* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

32 lines of code changed in 3 files:

• SL/PTCLEAN: Makefile (+1), ptclean.cxx (+30 -25), ptclean.h (+1 -1)

westram 2013-10-31 15:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2013-10-29 13:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2013-10-29 12:43 Rev.: 10954

- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2013-10-03 13:11 Rev.: 10704

- reintegrated branch 'helptest'

2 lines of code changed in 2 files:

• SL/PTCLEAN: Makefile (+1), ptclean.cxx (+1)

westram 2013-09-09 16:36 Rev.: 10563

- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

2 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+2)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1 -1)

westram 2013-02-09 13:52 Rev.: 9521

- updated depends for [9520]

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1)

westram 2013-02-09 12:16 Rev.: 9516

- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

• SL/PTCLEAN: Makefile (+1)

westram 2012-11-23 19:15 Rev.: 9226

* do not expect negations (in macro names)

1 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+1 -1)

westram 2012-11-23 18:58 Rev.: 9225

* rename unit test macros
- TEST_ASSERT.. -> TEST_EXPECT..

5 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+5 -5)

westram 2012-11-23 18:47 Rev.: 9224

* eliminated old TEST_ASSERT (pre-[8219]-style)
- replaced by new TEST_ASSERT (expecting expression equals true), TEST_ASSERT_NOTNULL or TEST_ASSERT_NONZERO

1 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+1 -1)

westram 2012-04-21 12:38 Rev.: 8641

* fixed warnings
- possible uninitialized variables
- DEBUG-mode variables
- ISLAND_HOPPING/Makefile: disabled warnings (i wont touch that module, except for removal)

1 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+1 -1)

westram 2012-04-19 20:26 Rev.: 8621

merge from e4fix [8340] [8341] [8342] [8343] [8344] [8345] [8346] [8347] [8348] [8349] [8350] [8353] [8354] [8362] [8370] [8371] [8372] [8373] [8374] [8375]

* changed refresh behavior
- refresh_all_windows
* call via timer (every 2 sec)
* replaced by refresh-requests where needed
* added ED4_trigger_instant_refresh
- set_refresh -> request_refresh
- removed duplicated refresh-request in ED4_consensus_definition_changed
- replaced ED4_refresh_window by ED4_request_full_refresh
* some callers now request fewer refreshes
* all callers now cause refresh of ALL windows
- ED4_cursor::!ShowCursor no longer updates global AWARs when used for display only
- refresh_window does not handle updates (it is only used to quickly draw the cursor)
* renamed into special_window_refresh() to disencourage usage
- removed implicit clearing of refresh flags previously done when refresh propagated down through windows, areas and hierarchy. Instead refresh_all_windows explicitely calls clear_refresh when done.
* cleaned up resize requests
* removed extra sync in ED4_resize_cb
* removed special handling of 1st call to ED4_expose_cb (no idea why, but this fixes an ancient bug: "save props in hide-all-gaps mode")
- no longer abuse ED4_expose_cb
* trigger relayout
- when helix/seq spacing is changed

* ED4_WinContext
- missing when NDS changed
- expect one in ED4_root::special_window_refresh
- provide from ED4_cursor::delete_cursor
* EDIT4 scrolling
- scrollbar code refactored
- SLIDER_OFFSET was missing in calculation of lower/right folding lines (fixed)
- picture size announced by ED4_window::update_scrolled_rectangle was off by 1
- fixed scroll/resize bugs introduced in [8618]
* added debug code
- print backtrace on negative folding line dimension
- print mismatch if slider postions and folding line dimensions are out of sync
* sequence color mapping
- fixed broken window layout
- increased number of sets to 8
* added symbolic ambiguity set as default
- hide default value '=0'
* group name generation (index-safety)
* execute callback-guards and post-useraction-callback whenever an awar change is directly triggered by a widget
* moved (ARB_)strNULLcmp to global header
* doc/fix unexpectable behavior (NULL is bigger that any text) with a test
* dont use magics for system folder

1 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+1 -1)

westram 2012-04-11 13:19 Rev.: 8574

* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

2 lines of code changed in 2 files:

• SL/PTCLEAN: needs_libs (new)

epruesse 2012-02-02 02:57 Rev.: 8351

keep a bit more data when cleaning an ARB DB for PT-server use
* the SAIs HELIX and HELIX_NR in addition to ECOLI
* all of presets/

We need the latter to keep the ARB file sufficiently complete to be opened
by arb_ntree. Previously, GBT_get_alignment_width would fail. NT_repair_DB
would cause a segmentation fault. Keeping all presets costs a bit of
memory/space, but the ability to open a database from lib/pts for
inspection seems more important than saving a few bytes (and fixing
NT_repair_DB much more difficult).

For the same reason, I think HELIX and HELIX_NR should be kept, as they
are expected by BI_helix. Since the cost is negligible, I'd argue for
keeping them just in case.

(Alternative solution, not pursued: always keep a cleaned and a full copy
of the ARB database in lib/pts, possibly changing the suffix on the
cleaned databases to express that they are no longer compatible)

4 lines of code changed in 1 file:

• SL/PTCLEAN: ptclean.cxx (+4 -6)

westram 2011-10-17 14:29 Rev.: 8103

merge from ptpan_back [8071] [8075] [8076] [8077] [8079]
* moved ARBDB/GB_system -> CORE/GBK_system
* moved basic file related functions from ARBDB to CORE
- GB_time_of_file (no longer automatically evaluates given path)

3 lines of code changed in 2 files:

• SL/PTCLEAN: Makefile (+1), ptclean.cxx (+2 -1)

westram 2011-10-07 14:39 Rev.: 8041

merge from dev [7990] [7991] [7992] [7993] [7994] [7995] [7996] [7998] [8001] [8003] [8005] [8006] [8007] [8008] [8009] [8011] [8012] [8019]
* added a faked ecoli to ptserver test-db
* added unit-tests for gene-ptserver
* rename ptserver testdb
* ptserver db-cleanup
- size of mapfile for SSUREF108 is reduced by 85% (3,4Gb -> 519Mb)
* ptserver
- refactored
* prefix tree builders
* probe_input_data
- removed ptnd_new_match (dead code)

243 lines of code changed in 6 files:

• SL/PTCLEAN: Makefile (new), ptclean.cxx (+166), ptclean.h (new)